Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching

Heterosis refers to the phenomenon where hybrids exhibit superior performance compared to the parental phenotypes and has been widely utilized in crossbreeding programs for animals and crops, yet the molecular mechanisms underlying this phenomenon remain enigmatic. A better understanding of the gene expression patterns in post-hatch chickens is very important for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens. In this study, breast muscle and liver tissues (n = 36) from full-sib F1 birds and their parental pure lines were selected to identify gene expression patterns and differentially expressed genes (DEGs) at 28 days of age by strand-specific RNA sequencing (ssRNA-seq). This study indicates that additivity is the predominant gene expression pattern in the F1 chicken post-hatch breast muscle (80.6% genes with additivity) and liver (94.2% genes with additivity). In breast muscle, Gene Ontology (GO) enrichment analysis revealed that a total of 11 biological process (BP) terms closely associated with growth and development were annotated in the identified DEG sets and non-additive gene sets, including STAT5A, TGFB2, FGF1, IGF2, DMA, FGF16, FGF12, STAC3, GSK3A, and GRB2. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation presented that a total of six growth- and development-related pathways were identified, involving key genes such as SLC27A4, GLUL, TGFB2, COX17, and GSK3A, including the PPAR signaling pathway, TGF-beta signaling pathway, and mTOR signaling pathway. Our results may provide a theoretical basis for crossbreeding in domestic animals.

Chronic Exposure to a PFAS Mixture Resembling AFFF-Impacted Surface Water Decreases Body Size in Northern Leopard Frogs (Rana pipiens)

Per- and polyfluoroalkyl substances (PFAS) occur in the environment as mixtures, yet mixture toxicity remains poorly understood. Aqueous film-forming foams (AFFFs) are a common source of PFAS. Our objective was to examine chronic effects of a complex PFAS mixture on amphibian growth and development. We tested toxicity of a five-chemical PFAS mixture summing to 10 μg/L and that accounts for >90% of the PFAS in AFFF-affected surface waters: perfluorooctane sulfonate (PFOS, 40%), perfluorohexane sulfonic acid (PFHxS, 30%), perflurooctanoic acid (PFOA, 12.5%), perfluorohexanoic acid (PFHxA, 12.5%), and perfluoropentanoic acid (PFPeA, 5%). We also included treatments to determine whether PFOS drove mixture toxicity and whether PFOS and mixture components act additively. We exposed Northern leopard frog (Rana pipiens) larvae through metamorphosis (∼130 d) in outdoor mesocosms. After 21 days of exposure, the larval body condition fell ∼5% relative to controls in the 4 μg/L PFOS treatment and mixtures lacking PFOS. At metamorphosis, the full 5-component 10 μg/L PFAS mixture reduced mass by 16% relative to controls. We did not observe effects on development. Our results indicate that toxicity of PFOS and other PFAS mixtures typical of AFFF sites act additively and that PFOS is not more inherently toxic than other mixture components.

Testing weak nulls in matched observational studies

We develop sensitivity analyses for the sample average treatment effect in matched observational studies while allowing unit-level treatment effects to vary. The methods may be applied to studies using any optimal without-replacement matching algorithm. In contrast to randomized experiments and to paired observational studies, we show for general matched designs that over a large class of test statistics, any procedure bounding the worst-case expectation while allowing for arbitrary effect heterogeneity must be unnecessarily conservative if treatment effects are actually constant across individuals. We present a sensitivity analysis which bounds the worst-case expectation while allowing for effect heterogeneity, and illustrate why it is generally conservative if effects are constant. An alternative procedure is presented that is asymptotically sharp if treatment effects are constant, and that is valid for testing the sample average effect under additional restrictions which may be deemed benign by practitioners. Simulations demonstrate that this alternative procedure results in a valid sensitivity analysis for the weak null hypothesis under a host of reasonable data-generating processes. The procedures allow practitioners to assess robustness of estimated sample average treatment effects to hidden bias while allowing for effect heterogeneity in matched observational studies.

New cup out of old coffee: contribution of parental gene expression legacy to phenotypic novelty in coffee beans of the allopolyploid Coffea arabica L

BACKGROUND AND AIMS

Allopolyploidization is a widespread phenomenon known to generate novel phenotypes by merging evolutionarily distinct parental genomes and regulatory networks in a single nucleus. The objective of this study was to investigate the transcriptional regulation associated with phenotypic novelty in coffee beans of the allotetraploid Coffea arabica.

METHODS

A genome-wide comparative transcriptomic analysis was performed in C. arabica and its two diploid progenitors, C. canephora and C. eugenioides. Gene expression patterns and homeologue expression were studied on seeds at five different maturation stages. The involvement of homeologue expression bias (HEB) in specific traits was addressed both by functional enrichment analyses and by the study of gene expression in the caffeine and chlorogenic acid biosynthesis pathways.

KEY RESULTS

Expression-level dominance in C. arabica seed was observed for most of the genes differentially expressed between the species. Approximately a third of the genes analysed showed HEB. This proportion increased during seed maturation but the biases remained equally distributed between the sub-genomes. The relative expression levels of homeologues remained relatively constant during maturation and were correlated with those estimated in leaves of C. arabica and interspecific hybrids between C. canephora and C. eugenioides. Functional enrichment analyses performed on genes exhibiting HEB enabled the identification of processes potentially associated with physiological traits. The expression profiles of the genes involved in caffeine biosynthesis mirror the differences observed in the caffeine content of mature seeds of C. arabica and its parental species.

CONCLUSIONS

Neither of the two sub-genomes is globally preferentially expressed in C. arabica seeds, and homeologues appear to be co-regulated by shared trans-regulatory mechanisms. The observed HEBs are thought to be a legacy of gene expression differences inherited from diploid progenitor species. Pre-existing functional divergences between parental species appear to play an important role in controlling the phenotype of C. arabica seeds.

Acute toxicity of pesticide mixtures to honey bees is generally additive, and well predicted by Concentration Addition

Understanding the frequency of non-additive effects of pesticides (synergism and antagonism) is important in the context of risk assessment. The goal of this study was to investigate the prevalence of non-additive effects of pesticides to honey bees (Apis mellifera). We investigated a large set of mixtures including insecticides and fungicides of different chemical modes of action and classes. The mixtures included represent a relevant sample of pesticides that are currently used globally. We investigated whether the experimental toxicity of the mixtures could be predicted based on the Concentration Addition (CA) model for acute contact and oral adult bee toxicity tests. We measured the degree of deviation from the additivity predictions of the experimental toxicity based on the well-known Mixture Deviation Ratio (MDR). Further, we investigated the appropriate MDR thresholds that should be used for the identification of non-additive effects based on acceptable rates for false positive (alpha) and true positive (beta) findings. We found that a deviation factor of MDR = 5 is a sound reference for labeling potential non-additive effects in acute adult bee experimental designs when assuming a typical Coefficient of Variation (CV%) = 100 in the determination of the LD₅₀ of a pesticide (a factor of 2× deviation in the LD ₅₀ resulting from inter-experimental variability). We found that only 2.4 % and 9 % of the mixtures evaluated had an MDR > 5 and MDR < 0.2, respectively. The frequency and magnitude of deviation from additivity found for bees in this study are consistent with those of other terrestrial and aquatic taxa. Our findings suggest that additivity is a good baseline for predicting the toxicity of pesticide mixtures to bees, and that the rare cases of synergy of pesticide mixtures to bees are not random but have a mechanistic basis.

Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma

Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm. While heterokaryosis dominates the life cycle of many fungal species, the transcriptomic changes associated with the transition from homokaryosis to heterokaryosis is not well understood. Here, we analyse gene expression profiles of homokaryons and heterokaryons from three phylogenetically and reproductively isolated lineages of the filamentous ascomycete Neurospora tetrasperma. We show that heterokaryons are transcriptionally distinct from homokaryons in the sexual stage of development, but not in the vegetative stage, suggesting that the phenotypic switch to fertility in heterokaryons is associated with major changes in gene expression. Heterokaryon expression is predominantly defined by additive effects of its two nuclear components. Furthermore, allele-specific expression analysis of heterokaryons with varying nuclear ratios show patterns of expression ratios strongly dependent on nuclear ratios in the vegetative stage. By contrast, in the sexual stage, strong deviations of expression ratios indicate a co-regulation of nuclear gene expression in all three lineages. Taken together, our results show two levels of expression control: additive effects suggest a nuclear level of expression, whereas co-regulation of gene expression indicate a heterokaryon level of control.

Bayesian unanchored additive models for component network meta-analysis

Component network meta-analysis (CNMA) models are an extension of standard network meta-analysis (NMA) models which account for the use of multicomponent treatments in the network. This article contributes innovatively to several statistical aspects of CNMA. First, by introducing a unified notation, we establish that currently available methods differ in the way they assume additivity, an important distinction that has been overlooked so far in the literature. In particular, one model uses a more restrictive form of additivity than the other which we term an anchored and unanchored model, respectively. We show that an anchored model can provide a poor fit to the data if it is misspecified. Second, given that Bayesian models are often preferred by practitioners, we develop two novel unanchored Bayesian CNMA models presented under the unified notation. An extensive simulation study examining bias, coverage probabilities, and treatment rankings confirms the favorable performance of the novel models. This is the first simulation study to compare the statistical properties of CNMA models in the literature. Finally, the use of our novel models is demonstrated on a real dataset, and the results of CNMA models on the dataset are compared.

[Constructing biomass models for natural Quercus mongolica based on Bayesian seemingly unrelated regression]

In this study, the biomass models for natural Quercus mongolica in Heilongjiang Province were constructed based on the predictors of diameter at breast height (D) and tree height (H) by several methods including multivariate likelihood analysis and seemingly unrelated regression. The results showed that the H could significantly improve the stem biomass model, with the coefficient of determination (R²) being increased from 0.953 to 0.988 and the root mean square error (RMSE) being reduced by 14 kg, but it had no significant improvement for the biomass model of branch, foliage, and root. The error structures of both biomass model systems (only D and D-H) were multiplicative, indicating that the linear models after logarithmic transformation were more appropriate. The R² for the biomass models of stem, branch, foliage and root were 0.953-0.988, 0.982-0.983, 0.916-0.917, and 0.951-0.952, while the RMSE were 13.42-27.03, 6.84-7.00, 1.95-1.97 and 9.71-9.84 kg. Compared with the feasible generalized least squares (FGLS) approach, Bayesian estimation had similar fitting performance and provided parameter estimates with different variations. The standard errors of parameters for FGLS were 0.054-0.211. There were similar variations (standard deviations of 0.055-0.221) for the two Bayesian estimation with no prior information (DMC and Gibbs1). The Gibbs sampler with a multivariate normal distribution with a mean vector of 0, variances of 1000 and covariances of 0 (Gibbs2) or the prior information from the historical researches summary for Quercus trees biomass models (Gibbs3) produced greater variation than those of FGLS, DMC, and Gibbs1 (stan-dard deviations were 0.080-0.278), while Gibbs sampler with the prior information obtained from own data (Gibbs4) provided the lower variations than others (standard deviations were 0.004-0.013). The Gibbs4 approach provided the narrowest 95% prediction interval and produced the smaller prediction biases, with the average absolute error percentage (MAPE) for stem, branch, foliage, root and total of the only-D biomass model being 19.8%, 24.7%, 24.6%, 29.0% and 13.1%, while MAPE for the corresponding components of D-H biomass model kept same except for stem and total decreased to 10.5% and 9.8%, which indicated that Gibbs4 could provide more accurate biomass predictions. Compared with classical statistics, accurate prior information made Bayesian seemingly unrelated regression an advantage in estimation stability and uncertainty reduction.

MiXie, an Online Tool for Better Health Assessment of Workers Exposed to Multiple Chemicals

There is increasing concern for workers facing multiple chemical exposure. The accumulation of information on occupational conditions indicates the need to incorporate the concept of multiple exposures in the risk assessment process and to develop tools for assessing the potential impacts of multiple exposures on workers’ health. Our objective is to describe the MiXie online decision-making tool that can be used to assess the risk of exposure to multiple chemicals. The description includes the development of MiXie, the structure of its toxicological database according to the target organ or the mode of action, and the algorithm for quantitative analysis of a mixture. Two case studies of its use in evaluating the risks of multiple exposures in real workplace situations are presented. The case study in the printing industry showed increased risk for four toxicological classes (central nervous system damage, ocular damage, skin damage, and ototoxicity) associated with co-exposure to four chemicals during maintenance operations. The MiXie analysis also showed the presence of carcinogenic substances in the mixture and a risk to the development of the foetus. The case study in nail salons showed the presence of carcinogenic and sensitizing chemicals and an increased risk to upper airways. MiXie helps preventers evaluate the possible additive effects of mixtures, providing an easy-to-read diagnosis to identify risks incurred by co-exposed employees. In addition, MiXie identifies risky occupational situations that would go unnoticed without a multiple substance approach.

How do humans group non-rigid objects in multiple object tracking?: Evidence from grouping by self-rotation

Previous studies on perceptual grouping found that people can use spatiotemporal and featural information to group spatially separated rigid objects into a unit while tracking moving objects. However, few studies have tested the role of objects' self-motion information in perceptual grouping, although it is of great significance to the motion perception in the three-dimensional space. In natural environments, objects always move in translation and rotation at the same time. The self-rotation of the objects seriously destroys objects' rigidity and topology, creates conflicting movement signals and results in crowding effects. Thus, this study sought to examine the specific role played by self-rotation information on grouping spatially separated non-rigid objects through a modified multiple object tracking (MOT) paradigm with self-rotating objects. Experiment 1 found that people could use self-rotation information to group spatially separated non-rigid objects, even though this information was deleterious for attentive tracking and irrelevant to the task requirements, and people seemed to use it strategically rather than automatically. Experiment 2 provided stronger evidence that this grouping advantage did come from the self-rotation per se rather than surface-level cues arising from self-rotation (e.g. similar 2D motion signals and common shapes). Experiment 3 changed the stimuli to more natural 3D cubes to strengthen the impression of self-rotation and again found that self-rotation improved grouping. Finally, Experiment 4 demonstrated that grouping by self-rotation and grouping by changing shape were statistically comparable but additive, suggesting that they were two different sources of the object information. Thus, grouping by self-rotation mainly benefited from the perceptual differences in motion flow fields rather than in deformation. Overall, this study is the first attempt to identify self-motion as a new feature that people can use to group objects in dynamic scenes and shed light on debates about what entities/units we group and what kinds of information about a target we process while tracking objects.

Synergism versus Additivity: Defining the Interactions between Common Disinfectants

Many of the most common disinfectant and sanitizer products are formulations of multiple antimicrobial compounds. Products claiming to contain synergistic formulations are common, although there is often little supporting evidence. The antimicrobial interactions of all pairwise combinations of common disinfectants (benzalkonium chloride, didecyldimethylammonium chloride, polyhexamethylene biguanide, chlorocresol, and bronopol) were classified via checkerboard assay and validated by time-kill analyses. Combinations were tested against Acinetobacter baumannii NCTC 12156, Enterococcus faecalis NCTC 13379, Klebsiella pneumoniae NCTC 13443, and Staphylococcus aureus NCTC 13143. Synergistic interactions were identified only for the combinations of chlorocresol with benzalkonium chloride and chlorocresol with polyhexamethylene biguanide. Synergism was not ubiquitously demonstrated against all species tested and was on the borderline of the synergism threshold. These data demonstrate that synergism between disinfectants is uncommon and circumstantial. Most of the antimicrobial interactions tested were characterized as additive. We suggest that this is due to the broad, nonspecific mechanisms associated with disinfectants not providing an opportunity for the combined activities of these compounds to exceed the sum of their parts.

Aquatic Toxicity Calculation of Mixtures: A Chemical Activity Approach Incorporating a Bioavailability Reduction Concept

A calculation estimating the effect concentration (EL/LL50) of a water-accommodated fraction (WAF) for mixture toxicity is proposed. The method is based on chemical activity where the activity of a molecule is its effective concentration taking into account intermolecular interactions. First, the thermodynamic influence of each constituent on the solubility of the others within the mixture (i.e. the concentration of each constituent in the "loading rate") is determined. Then, the non-bioavailable fraction is determined and removed to calculate the true concentration of each constituent exerting toxicity. Finally, the loading rate is adjusted until the sum of activities of the bioavailable fractions is equal to the fraction-weighted average of toxic activity of each constituent. This process is a mechanistic interpretation of experimental WAF tests. The methodology has been validated comparing toxic loading rates of 13 reliable experimental WAF studies on fish, daphnids, and algae. The predictions were all within a factor of 2 of the study outcomes and can be considered as accurate as the laboratory studies. This is in contrast to the standard additivity method which consistently overestimates the toxicity of these mixtures by at least a factor of 2 up to over an order of magnitude or even more.

Synergy in Nanomedicine: What It Is Not, and What It Might Be

Interactions between nanoformulations delivering two or more drugs-or a drug and some other therapeutic modality-are often described as synergistic. In fact, synergy is a specific term of art, with important therapeutic implications. The term is often misused in the nanoscience literature. Here we discuss what synergy is and an approach to demonstrating it rigorously.

A static model for estimating energy content of compound feeds in a dynamic feed evaluation system

The objective of the study was to develop a static empirical model for the estimation of net energy content of compound feeds in a dynamic feeding system using net energy for lactation at 20 kg of dry matter intake/d (NEL20) values calculated by the Nordic Feed Evaluation System (NorFor) model. In the NorFor system, NEL20 is a standardized value used to describe net energy content of feeds. The static model would allow prediction of the net energy value of compound feeds without access to the input data needed for the dynamic models. Our hypothesis was that NEL20 values of compound feeds can be predicted using organic matter digestibility (in vitro) and chemical components of the compound feeds as input variables. For this, 75 compound feeds and their 108 associated ingredients were collected across Scandinavia for model development. The proposed best model for prediction of compound feed NEL20 included crude fat, neutral detergent fiber, digestible organic matter measured in vitro, and crude protein (urea corrected) as independent variables. Lack of additivity of chemical components between values analyzed directly in the compound feed and values calculated by the weighted sum of ingredients was detected as the main source of error in the model, emphasizing the importance of accurate chemical analysis and sampling practices. Results from practical use of the model show that it may be a valuable tool that could be used by several actors in the feeding sector using the NorFor system. Feed manufacturers could use it to monitor the net energy content in their final product, and farmers could use it to check the net energy content of the purchased compound feed. However, validation of this model against an independent set of samples is lacking in this study and its prediction performance should be further evaluated. The model will need recalibration if the feed parameters used in the dynamic model for the estimation of reference values change, as this would not be reflected in the predicted values of the created model.

In Vitro Co-Exposure to CeO2 Nanomaterials from Diesel Engine Exhaust and Benzo(a)Pyrene Induces Additive DNA Damage in Sperm and Cumulus Cells but Not in Oocytes

Benzo(a)pyrene (BaP) is a recognized reprotoxic compound and the most widely investigated polycyclic aromatic hydrocarbon in ambient air; it is widespread by the incomplete combustion of fossil fuels along with cerium dioxide nanomaterials (CeO₂ NMs), which are used in nano-based diesel additives to decrease the emission of toxic compounds and to increase fuel economy. The toxicity of CeO₂ NMs on reproductive organs and cells has also been shown. However, the effect of the combined interactions of BaP and CeO₂ NMs on reproduction has not been investigated. Herein, human and rat gametes were exposed in vitro to combusted CeO₂ NMs or BaP or CeO₂ NMs and BaP in combination. CeO₂ NMs were burned at 850 °C prior to mimicking their release after combustion in a diesel engine. We demonstrated significantly higher amounts of DNA damage after exposure to combusted CeO₂ NMs (1 µg·L^-1) or BaP (1.13 µmol·L^-1) in all cell types considered compared to unexposed cells. Co-exposure to the CeO₂ NMs-BaP mixture induced additive DNA damage in sperm and cumulus cells, whereas no additive effect was observed in rat oocytes. This result could be related to the structural protection of the oocyte by cumulus cells and to the oocyte's efficient system to repair DNA damage compared to that of cumulus and sperm cells.

NMR study of dyadic and triadic splitting in copoly(arylene)phthalides based on diphenyl oxide and diphenyl sulfide

All ¹³ C NMR signals of the poly(arylene) polymers, O-1, S-7, OS-4, OOS-3, OOOS-2, SSO-5, and SSSO-6 (where O is a diphenyleneoxiphthalide unit and S is a diphenylenethiophthalide unit) in dyads and triads were assigned unequivocally with two-dimensional NMR techniques (ge-2D [¹ H-¹ H] COSY, ge-2D [¹ H-¹³ C] HSQC, and ge-2D [¹ H-¹³ C] HMBC), and for each atom, the increments of the shifts are determined. For structurally similar carbon atoms of the phthalide cycle and heteroaromatic fragments of the skeletal chain, additive signal splitting schemes in phthalide centered dyads and in diphenylene oxide and in diphenylene sulfide centered triads are considered, based on taking into account the contributions to their shielding of adjacent and distant substituents. It was shown that the nature of the splitting of the signals of each of the 20 carbon atoms in 3,3-bisphenylphthalide fragments is determined by the type of carbon atom (tertiary or quaternary, even or odd), the type of heteroatoms in adjacent heteroaromatic fragments, their distance from the identified carbon nucleus, and their polyad symmetry. The results obtained in this article will greatly facilitate our further studies and, in particular, will allow us to study the microstructure of statistical copolymers based on the asymmetric OS monomer at the dyad and triad levels.

Meta-analysis of multiple driver effects on marine phytoplankton highlights modulating role of pCO2

Responses of marine primary production to a changing climate are determined by a concert of multiple environmental changes, for example in temperature, light, pCO₂ , nutrients, and grazing. To make robust projections of future global marine primary production, it is crucial to understand multiple driver effects on phytoplankton. This meta-analysis quantifies individual and interactive effects of dual driver combinations on marine phytoplankton growth rates. Almost 50% of the single-species laboratory studies were excluded because central data and metadata (growth rates, carbonate system, experimental treatments) were insufficiently reported. The remaining data (42 studies) allowed for the analysis of interactions of pCO₂ with temperature, light, and nutrients, respectively. Growth rates mostly respond non-additively, whereby the interaction with increased pCO₂ profusely dampens growth-enhancing effects of high temperature and high light. Multiple and single driver effects on coccolithophores differ from other phytoplankton groups, especially in their high sensitivity to increasing pCO₂ . Polar species decrease their growth rate in response to high pCO₂ , while temperate and tropical species benefit under these conditions. Based on the observed interactions and projected changes, we anticipate primary productivity to: (a) first increase but eventually decrease in the Arctic Ocean once nutrient limitation outweighs the benefits of higher light availability; (b) decrease in the tropics and mid-latitudes due to intensifying nutrient limitation, possibly amplified by elevated pCO₂ ; and (c) increase in the Southern Ocean in view of higher nutrient availability and synergistic interaction with increasing pCO₂ . Growth-enhancing effect of high light and warming to coccolithophores, mainly Emiliania huxleyi, might increase their relative abundance as long as not offset by acidification. Dinoflagellates are expected to increase their relative abundance due to their positive growth response to increasing pCO₂ and light levels. Our analysis reveals gaps in the knowledge on multiple driver responses and provides recommendations for future work on phytoplankton.

Additivity of apparent and standardized ileal digestibility of phosphorus in mixed diets containing corn and soybean meal fed to broiler chickens

Phosphorus (P) is an integral part of diet formulation for broiler chickens as P is required for various biochemical processes essential to life. A study was designed to examine the additivity of apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of P in mixed diets containing corn and soybean meal (SBM) with or without phytase supplementation. Birds were fed a commercial starter diet from day 0 to 21 after hatching and then allotted to 7 dietary treatments in a randomized complete block design with the BW as a blocking factor. Four semipurified diets were prepared to contain corn or SBM as the sole source of P with or without the addition of phytase at 1,000 phytase units/kg of diet. Two mixed diets were also prepared to contain corn and SBM with or without the addition of phytase at 1,000 phytase units/kg diet. A P-free diet (PFD) was formulated to determine the basal ileal endogenous loss of P. There were 16 replicate cages of the PFD and 8 replicate cages of the 6 experimental diets, with 8 birds per replicate cage for a total of 512 birds. Diets were fed for 3 d. The ileal digesta of birds were collected from the distal two-thirds of the ileum on day 24 after hatching. The SID of P in corn and SBM were 52.2 and 65.4%, respectively (SEM = 1.37). The addition of phytase improved (P < 0.05) both the AID and SID of P in the corn, SBM, and mixed diets. The determined AID or SID in the corn and SBM with or without phytase was used to predict the AID or SID in the mixed diets. There were no differences between the predicted and determined digestibility values in the mixed diets for either AID or SID of P and thus additive. Phytase supplementation of the mixed diet did not influence the additivity of AID or SID. In conclusion, the AID or SID of P in the corn and SBM was additive in the mixed diets containing corn and SBM with or without the addition of phytase.

Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water

Folding and other protein self-assembly processes are driven by favorable interactions between O, N, and C unified atoms of the polypeptide backbone and side chains. These processes are perturbed by solutes that interact with these atoms differently than water does. Amide NH···O=C hydrogen bonding and various π-system interactions have been better characterized structurally or by simulations than experimentally in water, and unfavorable interactions are relatively uncharacterized. To address this situation, we previously quantified interactions of alkyl ureas with amide and aromatic compounds, relative to interactions with water. Analysis yielded strengths of interaction of each alkylurea with unit areas of different hybridization states of unified O, N, and C atoms of amide and aromatic compounds. Here, by osmometry, we quantify interactions of 10 pairs of amides selected to complete this dataset. An analysis yields intrinsic strengths of six favorable and four unfavorable atom-atom interactions, expressed per unit area of each atom and relative to interactions with water. The most favorable interactions are sp2O-sp2C (lone pair-π, presumably n-π*), sp2C-sp2C (π-π and/or hydrophobic), sp2O-sp2N (hydrogen bonding) and sp3C-sp2C (CH-π and/or hydrophobic). Interactions of sp3C with itself (hydrophobic) and with sp2N are modestly favorable, while sp2N interactions with sp2N and with amide/aromatic sp2C are modestly unfavorable. Amide sp2O-sp2O interactions and sp2O-sp3C interactions are more unfavorable, indicating the preference of amide sp2O to interact with water. These intrinsic interaction strengths are used to predict interactions of amides with proteins and chemical effects of amides (including urea, N-ethylpyrrolidone [NEP], and polyvinylpyrrolidone [PVP]) on protein stability.

Additivity of apparent and standardised ileal digestibility of phosphorus in corn and canola meal mixed diets; basal endogenous loss of phosphorus responses to phytase and age in broiler chickens

1. The additivity of apparent ileal digestibility (AID) and standardised ileal digestibility (SID) of phosphorus (P) in mixed diets containing corn and canola meal (CCM) with or without phytase supplementation and the impact of age on the basal ileal endogenous loss (BEL) of P were investigated in broiler chickens.2. Treatments were arranged as a 2 × 3 × 2 factorial with two ages (13 d or 21 d post hatching), three diets (corn, canola meal, or CCM), and two phytase levels (0 or 1,000 FYT/kg diet) in a randomised complete block design. There were eight or six birds per cage at 13 d and 21 d of age, respectively, and six replicate cages per treatment, with a total of 588 birds. A P-free diet (PFD) treatment was included at each age to determine the basal endogenous loss (BEL) of P.3. Birds were fed a commercial starter diet from d 1 to d 10 or d 18 and then fed the experimental diets for 3 d until d 13 or d 21, respectively. Predicted digestibility values calculated from the individual feed ingredients were used to test additivity in the mixed diets. Chromium oxide was included in diets as an indigestible marker.4. The ileal digesta, collected from birds at d 13 or d 21, was used to determine nutrient digestibility.5. The AID and SID of P at d 13 was higher (P < 0.01) when compared with older birds at d 21, regardless of dietary phytase supplementation. Regardless of age or phytase supplementation, AID and SID of P were additive, as there were no differences between predicted and determined values in the mixed diets. The BEL of P (g/kg DM intake) in birds at d 13 was higher (P < 0.05) than birds at d 21 (0.197 vs. 0.159).6. In conclusion, age had an impact on the BEL of P and the utilisation of minerals in the diets. The apparent and standardised ileal digestibility of P in the mixed diet containing corn and canola meal were additive, regardless of age or phytase supplementation.

No additive effect of combining sumatriptan and olcegepant in the GTN mouse model of migraine

INTRODUCTION

Despite recent advances in migraine treatment there is a need for therapies with higher clinical efficacy and/or fewer side effects. Triptans (5-HT_1B/1D/1F agonists) are essential in the present treatment regime and gepants (CGRP-receptor antagonists) are recognized as effective in acute migraine treatment. Triptans and gepants have different mechanisms of action and here we tested the hypothesis that a combination of these drugs (sumatriptan and olcegepant) would result in an additive effect.

METHODS

Using the validated glyceryl trinitrate mouse model of migraine, we initially tested dose-response relationships of sumatriptan (0.1, 0.3, and 0.6 mg/kg IP) and olcegepant (0.25, 0.50, and 1.0 mg/kg IP) to find suitable high and low doses. Subsequently, we performed a combination study of the two drugs with a low and a high dose. All experiments were vehicle (placebo) controlled and blinded.

RESULTS

Sumatriptan significantly reduced glyceryl trinitrate-induced allodynia (F(4,54) = 13.51, p < 0.0001) at all doses. Olcegepant also reduced glyceryl trinitrate-induced allodynia (F(4,53) = 16.11, p < 0.0001) with the two higher doses being significantly effective. Combining 0.50 mg/kg olcegepant with 0.1 or 0.6 mg/kg sumatriptan did not have any improved effect compared to either drug alone (p > 0.50 on all days) in our mouse model.

CONCLUSION

Combining olcegepant and sumatriptan did not have an additive effect compared to single-drug treatment in this study. Triptan-gepant combinations will therefore most likely not improve migraine treatment. Nevertheless, further studies are necessary, and combinations should also be examined in patients with migraine.

Phenotypic expression of floral traits in hybrid zones provides insights into their genetic architecture

Information on the genetic architecture of phenotypic traits is helpful for constructing and testing models of the ecoevolutionary dynamics of natural populations. For plant groups with long life cycles there is a lack of line cross experiments that can unravel the genetic architecture of loci underlying quantitative traits. To fill this gap, we propose the use of variation for phenotypic traits expressed in natural hybrid zones as an alternative approach. We used data from orchid hybrid zones and compared expected and observed patterns of phenotypic trait expression in different early-generation hybrid classes identified by molecular genetic markers. We found evidence of additivity, dominance, and epistatic interactions for different phenotypic traits. We discuss the potential of this approach along with its limitations and suggest that it may represent a realistic way to gain an initial insight into the heritability and genomic architecture of traits in organismal groups with complex life history, such as orchids and many others.

Combinatory Treatment with Oseltamivir and Itraconazole Targeting Both Virus and Host Factors in Influenza A Virus Infection

Influenza virus infections and their associated morbidity and mortality are a major threat to global health. Vaccination is an effective influenza prevention measure; however, the effectiveness is challenged by the rapid changes in the influenza virus genome leading to viral adaptation. Emerging viral resistance to the neuraminidase inhibitor oseltamivir limits the treatment of acute influenza infections. Targeting influenza virus-host interactions is a new and emerging field, and therapies based on the combination of virus- and host-directed drugs might significantly improve treatment success. We therefore assessed the combined treatment with oseltamivir and the repurposed antifungal drug itraconazole on infection of polarized broncho-epithelial Calu-3 cells with pdm09 or Panama influenza A virus strains. We detected significantly stronger antiviral activities in the combined treatment compared to monotherapy with oseltamivir, permitting lower concentrations of the drug than required for the single treatments. Bliss independence drug interaction analysis indicated that both drugs acted independently of each other. The additional antiviral effect of itraconazole might safeguard patients infected with influenza virus strains with heightened oseltamivir resistance.

Toward standardized amino acid matrices for exogenous phytase and protease in corn-soybean meal-based diets for broilers

A total of 468 male Ross 308 broilers were used in a digestibility study to determine the additivity of apparent or standardized amino acid (AA) digestibility values for corn, soybean meal (SBM), or a mixture of corn and SBM that were supplemented, or not, with either phytase, protease, or a combination of phytase and protease. These treatments generated a total of 12 experimental diets that were arranged in a 3 × 4 design. A nitrogen-free diet was also fed to estimate endogenous AA loss. Apparent and standardized AA digestibility values were assessed on day 28 posthatch. The apparent digestibility of AA in the complete diet was higher (P < 0.05) than expected based on the digestibility of the corn and SBM individually. However, this overestimation was corrected by the adjustment to standardized values. Importantly, addition of protease or the combination of protease and phytase increased (P < 0.05) the digestibility of AA in corn and SBM. Furthermore, these effects were arithmetically coherent with respect to the measured effects of the enzymes in the mixture of corn and SBM, even improving the additivity of AA digestibility values when assessed on an apparent basis. This study demonstrates that the effect of exogenous protease and phytase on AA digestibility in complete diets is predictable based on measurements made in individual ingredients. In addition to improving digestibility values per se, exogenous protease and phytase may enhance precision in least cost formulation systems.

Additivity of Ileal Amino Acid Digestibility in Diets Containing Corn, Soybean Meal, and Corn Distillers Dried Grains with Solubles for Male Broilers

The aim was to test additivity of apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of amino acids (AAs) in mixed diets for Ross 308 broiler chickens. Two hundred and eighty-eight, 20-d-old male broiler chickens were assigned to one of six diets, with six birds per cage using a randomized complete block design. The diets consisted of a nitrogen-free diet, three diets containing corn, soybean meal (SBM), and corn distillers dried grains with solubles (CDDGS) as the sole source of nitrogen, respectively, and two mixed diets containing corn, SBM or CDDGS. Chromic oxide was added to the diets as an indigestible index. On day 24, birds were euthanized for ileal digesta collection. Relative proportion of the basal endogenous loss of AAs to total ileal outflow of AAs in corn was greater (p < 0.05) than that of SBM and CDDGS. For the corn-SBM and corn-SBM-CDDGS mixed diets, the AID of AAs differed (p < 0.05) from the predicted values. No difference was observed between the measured and predicted SID of AA. In conclusion, the SID of AAs is more additive in mixed diets containing corn, SBM, or CDDGS compared to AID values.

Influence of feeding sunflower seed and meal protected against ruminal fermentation on ruminal fermentation, bacterial composition and in situ degradability in sheep

The effects of treating sunflower seed (SS) and meal (SM), as well as of a mixture of both feeds (SSM; 45:55) with a solution of malic acid (1 M; 400 ml/kg feed) and heating for protection against ruminal degradation were studied. Four rumen-fistulated sheep were fed two mixed diets composed of oat hay and concentrate (40:60) and differing only in the concentrate, that contained either a mixture of untreated SS and SM (control diet) or treated SS and SM (MAH diet). A crossover design with two 24-d experimental periods was used, and each period included 10 d of diet adaptation, 9 d for in situ incubations of SS, SM and SSM, and 5 d for measuring ruminal fermentation characteristics and rumen emptying. From day 6 onwards a solution of (¹⁵NH₄)₂SO₄ was continuously infused into the rumen of each sheep to label ruminal bacteria. Feeding the MAH diet did not affect either ruminal pH or concentrations of total volatile fatty acids and NH₃-N, but decreased (p ≤ 0.01) the molar proportions of acetate and propionate and increased those of butyrate (p< 0.001). Organic matter and lipid contents of ruminal bacteria were lower whereas both N content and ¹⁵N enrichment were greater (p ≤ 0.05) in MAH-fed sheep. The in situ effective degradability (ED) of different fractions of SS, SM and SSM were calculated from the ruminal rates of particle comminution and passage, and values were corrected for microbial contamination. The MAH treatment decreased the ED of most fractions for all feeds and increased the supply of by-pass crude protein (CP) by 19.1% and 120% for SS and SM, respectively, and that of fat by 34% for SS. The MAH treatment also increased the in vitro intestinal digestibility of the by-pass CP for both SS (from 60.1% to 75.4%) and SM (from 83.2% to 91.0%). The simultaneous heating of both feeds (SSM) reinforced the protective effect of the MAH treatment and increased the by-pass CP without altering its intestinal digestibility, increasing the intestinally digested CP content by 16.8% compared with the value estimated from the results obtained for MAH-treated SS and SM incubated independently. These results indicate that the MAH treatment was effective to protect sunflower protein against rumen degradation and increased its intestinal digestibility.

Ruminal fermentation characteristics and related feeding values of compound feeds and their constituting single feeds studied by using in vitro techniques

Single concentrate feeds are mixed together forming compound feeds for cattle. However, knowledge regarding the potential interactions (associative effects) between the feeding values of single feeds in compound feeds is lacking. The main objective of the present study was to evaluate ruminal fermentation characteristics and feeding values of eight industrially produced compound feeds in mash form from their constituent single feeds for dairy cows through in vitro assays. Additivity was given for gas production (GP), digestibility of organic matter (dOM) and utilisable CP at the duodenum (uCP). Additivity of CP fractions (determined using the Cornell Net Carbohydrate and Protein System (CNCPS)) was dependent on the fraction and compound feed type; however, the effective degradation calculated from CP fractions (EDCNCPS) showed additivity. Additivity was not given for intestinal digestibility of rumen-undegraded protein (IDRUP) for five out of eight compound feeds. Precise calculation of metabolisable energy (ME) of compound feeds from ME of single feeds was possible when using the same ME equations for all single and compound feeds. Compound feeds are often provided in pellet form; therefore, our second objective was to evaluate the effects of pelleting on ruminal fermentation characteristics and feeding values of compound feeds. Pelleting affected GP at 24 h (GP24; up to 2.4 ml/200 mg DM), dOM (up to 2.3 percentage point (pp)) and ME (up to 0.3 MJ/kg DM), but these differences were overall small. More considerable effects of pelleting were observed for uCP, which was increased in all compound feeds except the two with the highest CP concentrations. The IDRUP was lower in most compound feeds following pelleting (up to 15 pp). Pelleting also affected CP fractions in a non-systematic way. Overall, the effects of pelleting were not considerable, which could be because pelleting conditions were mild. Our third objective was to compare in situ ruminal CP degradation (EDIN_SITU) of compound feeds with ED using two prediction methods based on CP fractions. EDIN_SITU reference data were obtained from a companion study using the same feeds. Prediction accuracy of EDIN_SITU and EDCNCPS was variable and depended on the compound feed and prediction method. However, future studies are needed as to date not enough data are published to draw overall conclusions for the prediction of EDIN_SITU from CP fractions.

Additive Contact Polarization of Nonferroelectric Polymers for Patterning of Multilevel Memory Elements

When a thin polymer film supported by a conductive substrate is contacted by and then separated from a micropatterned polymeric stamp, the so-called contact electrification creates electrical charges over the stamped regions. Simultaneously, image charges are induced in the conductive substrate. Together, the surface and image charges establish large fields within the film, in effect polarizing it. Upon consecutive stampings, the magnitudes of polarization add up, enabling imprinting of multilevel polarization patterns. Because the electric field is high only within the film but low across the Gaussian surface surrounding the film/substrate system, the discharge of surface charges is slow and the polarization patterns are relatively long-lived. These findings are significant since multilevel polarization states have, to date, been achieved only in ferroelectrics or some specialized polymers-the current method extends them to common polymers such as poly(methyl methacrylate), poly(vinyl pyrrolidone), or poly(vinyl acetate).

Assessing the Potential for Interaction in Insecticidal Activity Between MON 87751 × MON 87701 Produced by Conventional Breeding

Pyramiding (combining) of plant incorporated protectants (PIPs) with insecticidal activity in genetically engineered crops is a strategy used to improve efficacy as well as delay potential resistance for a specific group of targets. In some countries, a regulatory risk assessment is required for breeding "stacks" expressing multiple PIPs and these countries may require an assessment of potential interaction among the PIPs. This study evaluated whether combining soybean events MON 87551 and MON 87701 results in a toxicological interaction that effects a species that is controlled by each event. MON 87751 coexpresses the Cry1A.105 and Cry2Ab2 proteins and MON 87701 expresses the Cry1Ac protein. EC50 values for MON 87751 and MON 87701 were comparable in diet-incorporation bioassays using corn earworm (Lepidoptera: Noctuidae, Helicoverpa zea) and the observed combined activity of the stack was consistent with predictions of additivity (i.e., no interaction). Under the concentration and response addition models, predicted and observed median effect levels differed by <10%. These results demonstrate independent action at the median effect level between the insecticidal activity of MON 87751 and MON 87701. Taken together, no interaction between these PIPs and acceptable margins of safety for the individual proteins to nontarget organisms, it is appropriate to bridge back to the risk assessments for the individual products that demonstrated environmental safety of stack products containing both MON 87751 and MON 87701.

Limits to Compensatory Mutations: Insights from Temperature-Sensitive Alleles

Previous experiments with temperature-sensitive mutants of the yeast enzyme orotidine 5'-phosphate decarboxylase (encoded in gene URA3) yielded the unexpected result that reversion occurs only through exact reversal of the original mutation (Jakubowska A, Korona R. 2009. Lack of evolutionary conservation at positions important for thermal stability in the yeast ODCase protein. Mol Biol Evol. 26(7):1431-1434.). We recreated a set of these mutations in which the codon had two nucleotide substitutions, making exact reversion much less likely. We screened these double mutants for reversion and obtained a number of compensatory mutations occurring at alternative sites in the molecule. None of these compensatory mutations fully restored protein performance. The mechanism of partial compensation is consistent with a model in which protein stabilization is additive, as the same secondary mutations can compensate different primary alternations. The distance between primary and compensatory residues precludes direct interaction between the sites. Instead, most of the compensatory mutants were clustered in proximity to the catalytic center. All of the second-site compensatory substitutions occurred at relatively conserved sites, and the amino acid replacements were to residues found at these sites in a multispecies alignment of the protein. Based on the estimated distribution of changes in Gibbs free energy among a large number of amino acid replacements, we estimate that, for most proteins, the probability that a second-site mutation would have a sufficiently large stabilizing effect to offset a temperature-sensitive mutation in the order of 10-4 or less. Hence compensation is likely to take place only for slightly destabilizing mutations because highly stabilizing mutations are exceeding rare.

Additivity of apparent and standardized ileal amino acid digestibility of corn and soybean meal in broiler diets

A total of 144 male Ross 308 broiler chickens were used in a digestibility bioassay to determine the additivity of apparent or standardized amino acid (AA) digestibility values for corn, soybean meal (SBM), or a mixture of corn and SBM. Following the receipt of a standard commercial starter diet from days 1 to 21, broilers were divided into 4 treatments (6 cages per treatment; 6 birds per cage) and received semi-purified diets based on corn, SBM, or a mixture of corn and SBM or a nitrogen-free diet (for the estimation of basal endogenous AA losses). Apparent and standardized ileal AA digestibility values were determined on day 28 and the measured values for the mixture of corn and SBM were statistically compared to calculated values based on the digestibility of the individual raw materials and their concentration in the mixed diet. The use of apparent ileal AA digestibility values for single ingredients resulted in an underestimation (P < 0.05) of the digestibility of the mixed feed for nitrogen, Lys, Arg, Thr, Asp, and Gly. Correction of apparent digestibility values to standardized values entirely corrected the underestimation in the mixed feed and resulted in a predictable linearity from single ingredients to the mixed diet. It can be concluded that standardized ileal AA digestibility values are more additive than apparent values and should be used, where possible, to enhance the accuracy of feed formulation and reduce both the diet cost and the environmental impact of nitrogenous pollution.

Additivity of apparent and standardized ileal digestibility of amino acids in wheat, canola meal, and sorghum distillers dried grains with solubles in mixed diets fed to broiler chickens

An experiment was conducted to investigate which method, apparent ileal digestibility (AID) or standardized ileal digestibility (SID), more accurately predicts the digestibility of crude protein (CP) and amino acids (AA) in mixed diets fed to broiler chickens. Male Ross 308 broiler chickens received a standard starter diet from d 0 to 16 post hatching, thereafter grouped into 8 blocks, based on body weight (BW), of 10 birds/cage, and randomly allotted to 6 diets in a randomized complete block design. The 6 diets consisted of a nitrogen-free diet, 3 semi-purified diets, and 2 mixed diets to test the additivity of AID and SID in mixed diets. On d 21 post hatching, digesta from two-thirds of the distal ileum was collected. Using the determined AID or SID for CP and AA in wheat, canola meal (CM), or sorghum distillers dried grains with solubles (DDGS), the AID or SID for 2 mixed diets based on wheat-CM or wheat-CM-DDGS were predicted and compared with determined AID or SID, respectively. The results revealed that the predicted SID of CP and AA in the wheat-CM mixed diet were consistent with determined values except for Asp and Ser, and all the predicted SID of CP and AA were consistent with the determined values in the wheat-CM-DDGS mixed diet. The determined AID of Ile, Met, Thr, Val, Ala, Cys, Ser, and Tyr in the wheat-CM mixed diet were greater (P < 0.05) than predicted AID values. For the wheat-CM-DDGS mixed diet, the determined AID of Trp, Cys, and Glu were greater (P < 0.05) than the predicted AID values. However, there were more inconsistencies between the determined and predicted values in AID values for wheat-CM than the wheat-CM-DDGS mixed diet than SID values for both diets. In conclusion, the present study confirmed that the SID of CP and AA was more additive than the AID of CP and AA when a mixed diet contained wheat, CM, and DDGS as protein sources in broiler chickens.

Pre-attentive Mismatch Response and Involuntary Attention Switching to a Deviance in an Earlier-Than-Usual Auditory Stimulus: An ERP Study

An acoustic stimulus elicits an electroencephalographic response called auditory event-related potential (ERP). When some members of a stream of standard auditory stimuli are replaced randomly by a deviant stimulus and this stream is presented to a subject who ignores the stimuli, two different ERPs to deviant and standard stimuli are recorded. If the ERP to standard stimuli is subtracted from the ERP to deviant stimuli, the difference potential (DP) waveform typically exhibits a series of negative-positive-negative deflections called mismatch negativity (MMN), P3a, and reorienting negativity (RON), which are associated with pre-attentive change detection, involuntary attention switching, and reorienting of attention, respectively. The aim of the present study was to investigate how these pre-attentive processes are affected if the change occurs earlier than its usual timing implied by isochronous standard stimuli. In the MMN paradigm employed, 15% of the standards were randomly replaced by deviant stimuli which differed either in their pitch, their earlier onset time, or in both. Event-related responses to these three deviants [timely pitch change (R_TP), earlier onset (R_EO), earlier pitch change (R_EP)] and to standards (R_S) were recorded from 10 reading subjects. To maintain identical stimulation histories for the responses subtracted from each other, "deviant-standard" difference potentials (DP) for "timely" and "early" pitch deviances were derived as follows: DP_TP = R_TP - R_S and DP_EP = R_EP - R_EO. Interestingly, the MMN components of the DPs to timely and early pitch deviances had similar amplitudes, indicating that regularity of stimulus timing does not provide any benefit for the pre-attentive auditory change detection mechanism. However, different scalp current density (SCD) dynamics of the MMN/P3a complexes, elicited by timely and early pitch deviances, suggested that an auditory change in a stimulus occurring earlier-than-usual initiates a faster and more effective call-for-attention and causes stronger attention switching than a timely change. SCD results also indicated that the temporal, frontal, and parietal MMN components are simultaneously present rather than emerging sequentially in time, supporting the MMN models based on parallel deviance processing in the respective cortices. Similarity of the RONs to timely and early pitch deviances indicated that reorienting of attention is of the same strength in two cases.

Additivity of standardized ileal digestibility of amino acids in mixed diets containing multiple protein sources for growing pigs fed three crude protein levels

This study was conducted to investigate the effect of dietary crude protein (CP) levels of semi-purified diets on the additivity of values for standardized ileal digestibility (SID) of amino acids (AA) in mixed diets from multiple protein sources for growing pigs. A total of 28 barrows (initial BW, 66.4 ± 1.3 kg) were surgically fitted with simple T-cannulas at the distal ileum and assigned to a replicated 14 × 4 incomplete Latin square design with 14 diets and 4 periods. The 14 experimental diets consisted of a nitrogen-free diet; a corn-based diet (80 g CP/kg); nine semi-purified diets containing soya bean meal (SBM), canola meal (CM) or corn distillers dried grains with solubles (cDDGS), each type (protein source) of semi-purified diets supplied 80, 120 or 160 g CP/kg, respectively; three mixed diets based on corn, SBM, CM and cDDGS formulated to contain 120, 160 and 200 g CP/kg respectively. Pigs were fed each of the 14 diets during a seven-day period, and ileal digesta were collected from 08:00 a.m to 6:00 p.m on day 6 and 7. Chromic oxide was added as an indigestible marker. Results indicated that the SID of CP and AA were not affected by CP levels (p > .05). Values for SID of AA were additive (p > .05) with the exception of His and Lys; Arg and Lys; Arg, Lys, Thr, Asp, Cys and Gly in the mixed diets containing 120, 160 and 200 g CP/kg respectively (p < .05). In conclusion, additivity of SID values of AA in the mixed diets at different CP levels was not affected by the CP levels of semi-purified diets for growing pigs. Therefore, it is recommended that SID values of AA should be used to formulate practical diets containing multiple ingredients for pigs.

Concentration-Dependent Synergy and Antagonism of Linezolid and Moxifloxacin in the Treatment of Childhood Tuberculosis: The Dynamic Duo

Background. No treatment regimens have been specifically designed for children, in whom tuberculosis is predominantly intracellular. Given their activity as monotherapy and their ability to penetrate many diseased anatomic sites that characterize disseminated tuberculosis, linezolid and moxifloxacin could be combined to form a regimen for this need.

Methods. We examined microbial kill of intracellular Mycobacterium tuberculosis (Mtb) by the combination of linezolid and moxifloxacin multiple exposures in a 7-by-7 mathematical matrix. We then used the hollow fiber system (HFS) model of intracellular tuberculosis to identify optimal dose schedules and exposures of moxifloxacin and linezolid in combination. We mimicked pediatric half-lives and concentrations achieved by each drug. We sampled the peripheral compartment on days 0, 7, 14, 21, and 28 for Mtb quantification, and compared the slope of microbial kill of Mtb by these regimens to the standard regimen of isoniazid, rifampin, and pyrazinamide, based on exponential decline regression.

Results. The full exposure-response surface identified linezolid-moxifloxacin zones of synergy, antagonism, and additivity. A regimen based on each of these zones was then used in the HFS model, with observed half-lives of 4.08 ± 0.66 for linezolid and 3.80 ± 1.34 hours for moxifloxacin. The kill rate constant was 0.060 ± 0.012 per day with the moxifloxacin-linezolid regimen in the additivity zone vs 0.083 ± 0.011 per day with standard therapy, translating to a bacterial burden half-life of 11.52 days vs 8.53 days, respectively.

Conclusions. We identified doses and dose schedules of a linezolid and moxifloxacin backbone regimen that could be highly efficacious in disseminated tuberculosis in children.

Linkage Analysis and Association Mapping QTL Detection Models for Hybrids Between Multiparental Populations from Two Heterotic Groups: Application to Biomass Production in Maize (Zea mays L.)

Identification of quantitative trait loci (QTL) involved in the variation of hybrid value is of key importance for cross-pollinated species such as maize (Zea mays L.). In a companion paper, we illustrated a new QTL mapping population design involving a factorial mating between two multiparental segregating populations. Six biparental line populations were developed from four founder lines in the Dent and Flint heterotic groups. They were crossed to produce 951 hybrids and evaluated for silage performances. Previously, a linkage analysis (LA) model that assumes each founder line carries a different allele was used to detect QTL involved in General and Specific Combining Abilities (GCA and SCA, respectively) of hybrid value. This previously introduced model requires the estimation of numerous effects per locus, potentially affecting QTL detection power. Using the same design, we compared this “Founder alleles” model to two more parsimonious models, which assume that (i) identity in state at SNP alleles from the same heterotic group implies identity by descent (IBD) at linked QTL (“SNP within-group” model) or (ii) identity in state implies IBD, regardless of population origin of the alleles (“Hybrid genotype” model). This last model assumes biallelic QTL with equal effects in each group. It detected more QTL on average than the two other models but explained lower percentages of variance. The “SNP within-group” model appeared to be a good compromise between the two other models. These results confirm the divergence between the Dent and Flint groups. They also illustrate the need to adapt the QTL detection model to the complexity of the allelic variation, which depends on the trait, the QTL, and the divergence between the heterotic groups.

Symmetry and additivity

All ¹ H and ¹³ C NMR signals of the four poly(phenylenephthalides): polydiphenylenephthalide (P(DPh)-1), polyterphenylenephthalide (P(TPh)-2) and two sequentially ordered polymers with different ratios of alternating diphenylenephthalide and terphenylenephthalide units (P(DTPh)-3, P(DDTPh)-4) were assigned unequivocally with two-dimensional NMR techniques (¹ H-¹ H COSY and NOESY; ¹ H-¹³ C HSQC and HMBC). There are four types of polyphenylene fragments: not symmetrical end, symmetrical inner, symmetrical pre-end and formally symmetric pre-end. The equivalent carbon atoms in these fragments have different chemical shifts. A full additivity of the chemical shifts for the side phthalide and polyphenylene carbon atoms was revealed. A new structure of diads with a mirror symmetry plane, passing through the middle of aromatic moieties, is proposed. Copyright © 2017 John Wiley & Sons, Ltd.

Reciprocal Genetics: Identifying QTL for General and Specific Combining Abilities in Hybrids Between Multiparental Populations from Two Maize (Zea mays L.) Heterotic Groups

Several plant and animal species of agricultural importance are commercialized as hybrids to take advantage of the heterosis phenomenon. Understanding the genetic architecture of hybrid performances is therefore of key importance. We developed two multiparental maize (Zea mays L.) populations, each corresponding to an important heterotic group (dent or flint) and comprised of six connected biparental segregating populations of inbred lines (802 and 822 lines for each group, respectively) issued from four founder lines. Instead of using "testers" to evaluate their hybrid values, segregating lines were crossed according to an incomplete factorial design to produce 951 dent-flint hybrids, evaluated for four biomass production traits in eight environments. QTL detection was carried out for the general-combining-ability (GCA) and specific-combining-ability (SCA) components of hybrid value, considering allelic effects transmitted from each founder line. In total, 42 QTL were detected across traits. We detected mostly QTL affecting GCA, 31% (41% for dry matter yield) of which also had mild effects on SCA. The small impact of dominant effects is consistent with the known differentiation between the dent and flint heterotic groups and the small percentage of hybrid variance due to SCA observed in our design (∼20% for the different traits). Furthermore, most (80%) of GCA QTL were segregating in only one of the two heterotic groups. Relative to tester-based designs, use of hybrids between two multiparental populations appears highly cost efficient to detect QTL in two heterotic groups simultaneously. This presents new prospects for selecting superior hybrid combinations with markers.

Response to comment on 'Randomization inference for treatment effects on a binary outcome'

We thank Professor Yasutaka Chiba [1 ] for commenting on Rigdon and Hudgens (RH) [2 ]. Chiba [1 ] described a certain exact confidence interval reported in RH as “somewhat unnatural.” Chiba also presented an alternative approach to constructing confidence intervals [3 ]. In this response, we (i) provide a simple explanation why the confidence interval in RH appeared “unnatural,” and (ii) explain the relationship between the RH [2 ] and Chiba [3 ] confidence intervals. Essentially the two approaches are equivalent, except RH entails inverting one two-sided test whereas Chiba inverts two one-sided tests. We present a more computationally efficient method (RLH) for computing the RH intervals based on Chiba’s principal stratification formulation of the problem. We also propose a third method based on Blaker [4 ] which inverts a single two-sided test but forms a confidence interval that is at least as narrow as inverting two one-sided tests. Simulation results show the RLH intervals tend to be as narrow or narrower than the Chiba and Blaker intervals on average.

Cytotoxic Effects of the Therapeutic Radionuclide Rhenium-188 Combined with Taxanes in Human Prostate Carcinoma Cell Lines

OBJECTIVE

Rhenium-188-HEDP is an effective radiopharmaceutical for the treatment of painful bone metastases from prostate cancer. The effectiveness of the β-radiation emitted by ¹⁸⁸Re might be enhanced by combination with chemotherapy, using the radiosensitization concept. Therefore, the authors investigated the combined treatment of the taxanes, docetaxel and cabazitaxel, with ¹⁸⁸Re in prostate carcinoma cell lines.

MATERIALS AND METHODS

The cytotoxic effects of single and combined treatment with taxanes and ¹⁸⁸Re were investigated in three human prostate carcinoma cell lines (PC-3, DU 145, and LNCaP), using the colony-forming assay. The half maximal effective concentration (EC50) of all individual agents was determined. The combined treatment was studied at 0.25, 0.5, 1, 2, and 4 times the EC50 of each agent. The interaction was investigated with a regression model.

RESULTS

The survival curves showed dose-dependent cell growth inhibition for both the taxanes and ¹⁸⁸Re. The regression model showed a good capability of explaining the data. It proved additivity in all combination experiments and confirmed a general trend to a slight subadditive effect.

CONCLUSIONS

This proof-of-mechanism study exploring radiosensitization by combining ¹⁸⁸Re and taxanes showed no synergism, but significant additivity. This encourages the design of in vivo studies. Future research should explore the potential added value of concomitant treatment of bone metastases with chemotherapy and ¹⁸⁸Re-HEDP.

Additivity of Feature-Based and Symmetry-Based Grouping Effects in Multiple Object Tracking

Multiple object tracking (MOT) is an attentional process wherein people track several moving targets among several distractors. Symmetry, an important indicator of regularity, is a general spatial pattern observed in natural and artificial scenes. According to the “laws of perceptual organization” proposed by Gestalt psychologists, regularity is a principle of perceptual grouping, such as similarity and closure. A great deal of research reported that feature-based similarity grouping (e.g., grouping based on color, size, or shape) among targets in MOT tasks can improve tracking performance. However, no additive feature-based grouping effects have been reported where the tracking objects had two or more features. “Additive effect” refers to a greater grouping effect produced by grouping based on multiple cues instead of one cue. Can spatial symmetry produce a similar grouping effect similar to that of feature similarity in MOT tasks? Are the grouping effects based on symmetry and feature similarity additive? This study includes four experiments to address these questions. The results of Experiments 1 and 2 demonstrated the automatic symmetry-based grouping effects. More importantly, an additive grouping effect of symmetry and feature similarity was observed in Experiments 3 and 4. Our findings indicate that symmetry can produce an enhanced grouping effect in MOT and facilitate the grouping effect based on color or shape similarity. The “where” and “what” pathways might have played an important role in the additive grouping effect.

Drug Combinations: Tests and Analysis with Isoboles

Described in this unit are experimental and computational methods to detect and classify drug interactions. In most cases, this relates to two drugs or compounds with overtly similar effects, e.g., two analgesics or two anti-hypertensives. From the dose-response data of the individual drugs, it is possible to generate a curve, the isobole, which defines all dose combinations that are expected to yield a specified effect. The theory underlying the isobole involves the calculation of doses of drug A that are effectively equivalent to doses of drug B with that equivalence determining whether the isobole is linear or nonlinear. In either case, the isobole allows for a comparison with actual combination effects making it possible to determine whether the interaction is synergistic, additive, or sub-additive. Actual as well as illustrative data are employed to demonstrate experimental design and data analysis.

Environmentally oriented models and methods for the evaluation of drug × drug interaction effects

This detailed review compares known and widely used methods for drug interaction estimation, some of which now have historical significance. Pharmaceutical application has been noted as far back as several thousand years ago. Relatively late in the 20th century, however, researchers became aware that their fate and metabolism, which still remain a great challenge for environmental analysts and risk assessors. For the patient's well-being, treatment based on the mixing of drugs has to be effective and should not cause any side effects (or side effects should not have a significant impact on health and mortality). Therefore, it is important to carefully examine drugs both individually and in combinations. It should be also stated that application form/way of entering the living organism is of great importance as well as the age and the place in the trophic system of the organism in order to eliminate harmful dosages in the case of infants' accidental intoxication.

Additivity and Interactions in Ecotoxicity of Pollutant Mixtures: Some Patterns, Conclusions, and Open Questions

Understanding the effects of exposure to chemical mixtures is a common goal of pharmacology and ecotoxicology. In risk assessment-oriented ecotoxicology, defining the scope of application of additivity models has received utmost attention in the last 20 years, since they potentially allow one to predict the effect of any chemical mixture relying on individual chemical information only. The gold standard for additivity in ecotoxicology has demonstrated to be Loewe additivity which originated the so-called Concentration Addition (CA) additivity model. In pharmacology, the search for interactions or deviations from additivity (synergism and antagonism) has similarly captured the attention of researchers over the last 20 years and has resulted in the definition and application of the Combination Index (CI) Theorem. CI is based on Loewe additivity, but focused on the identification and quantification of synergism and antagonism. Despite additive models demonstrating a surprisingly good predictive power in chemical mixture risk assessment, concerns still exist due to the occurrence of unpredictable synergism or antagonism in certain experimental situations. In the present work, we summarize the parallel history of development of CA, IA, and CI models. We also summarize the applicability of these concepts in ecotoxicology and how their information may be integrated, as well as the possibility of prediction of synergism. Inside the box, the main question remaining is whether it is worthy to consider departures from additivity in mixture risk assessment and how to predict interactions among certain mixture components. Outside the box, the main question is whether the results observed under the experimental constraints imposed by fractional approaches are a de fide reflection of what it would be expected from chemical mixtures in real world circumstances.

Nonadditive gene expression in polyploids

Allopolyploidy involves hybridization and duplication of divergent parental genomes and provides new avenues for gene expression. The expression levels of duplicated genes in polyploids can show deviation from parental additivity (the arithmetic average of the parental expression levels). Nonadditive expression has been widely observed in diverse polyploids and comprises at least three possible scenarios: (a) The total gene expression level in a polyploid is similar to that of one of its parents (expression-level dominance); (b) total gene expression is lower or higher than in both parents (transgressive expression); and (c) the relative contribution of the parental copies (homeologs) to the total gene expression is unequal (homeolog expression bias). Several factors may result in expression nonadditivity in polyploids, including maternal-paternal influence, gene dosage balance, cis- and/or trans-regulatory networks, and epigenetic regulation. As our understanding of nonadditive gene expression in polyploids remains limited, a new generation of investigators should explore additional phenomena (i.e., alternative splicing) and use other high-throughput "omics" technologies to measure the impact of nonadditive expression on phenotype, proteome, and metabolome.

Randomization inference for treatment effects on a binary outcome

Two methods are developed for constructing randomization-based confidence sets for the average effect of a treatment on a binary outcome. The methods are nonparametric and require no assumptions about random sampling from a larger population. Both of the resulting 1 - α confidence sets are exact in the sense that the probability of containing the true treatment effect is at least 1 - α. Both types of confidence sets are also guaranteed to have width no greater than one. In contrast, a previously proposed asymptotic confidence interval is not exact and may have width greater than 1. The first approach combines Bonferroni-adjusted prediction sets for the attributable effects in the treated and untreated. The second method entails inverting a permutation test. Simulations are presented comparing the two randomization-based confidence sets with the asymptotic interval as well as the standard Wald confidence interval and a commonly used exact interval for the difference in binomial proportions. Results show for small to moderate sample sizes that the permutation confidence set attains the narrowest width on average among the methods that maintain nominal coverage. Extensions that allow for stratifying on categorical baseline covariates are also discussed.

The emergence of scalar meanings

This paper analyzes the emergence of scalar additive meanings. We show that in Basque the same particle ere can obtain both the “simple additive” reading (akin to English too) and the “scalar additive” reading (akin to English even) but we argue that we do not have to distinguish two types of ere. We provide evidence, by means of a production and a perception experiment, that the reading is disambiguated by means of prosody (the placement of nuclear stress), which is a correlate of focus. We argue that the scalarity effect is generated by the combination of two presuppositions (a focus-induced one and a lexical one) and the assertion of the sentence.

Gene-expression novelty in allopolyploid cotton: a proteomic perspective

Allopolyploidization is accompanied by changes in gene expression that are thought to contribute to phenotypic diversification. Here we describe global changes in the single-celled cotton fiber proteome of two natural allopolyploid species (Gossypium hirsutum and G. barbadense) and living models of their diploid parents using two different proteomic approaches. In total, 1323 two-dimensional gel electrophoresis spots and 1652 identified proteins by isobaric tags for relative and absolute quantitation were quantitatively profiled during fiber elongation. Between allopolyploids and their diploid A- and D-genome progenitors, amounts of differential expression ranged from 4.4 to 12.8%. Over 80% of the allopolyploid proteome was additively expressed with respect to progenitor diploids. Interestingly, the fiber proteome of G. hirsutum resembles the parental A-genome more closely, where long, spinable fiber first evolved, than does the fiber proteome of G. barbadense. More protein expression patterns were A-dominant than D-dominant in G. hirsutum, but in G. barbadense, the direction of expression-level dominance switched from the D-genome to the A-genome during fiber development. Comparison of developmental changes between the two allopolyploid species revealed a high level of proteomic differentiation despite their shared ancestry, relatively recent evolutionary divergence, and similar gross morphology. These results suggest that the two allopolyploid species have achieved superficially similar modern fiber phenotypes through different evolutionary routes at the proteome level. We also detected homeolog-specific expression for 1001 proteins and present a novel approach to infer the relationship between homeolog-specific and duplicate expression patterns. Our study provides a proteomic perspective on understanding evolutionary consequences of allopolyploidization, showing how protein expression has been altered by polyploidization and subsequently has diversified among species.

Determination of additivity of apparent and standardized ileal digestibility of amino acids in diets containing multiple protein sources fed to growing pigs

An experiment was conducted in growing pigs to investigate the additivity of apparent ileal digestibility (AID) or standardized ileal digestibility (SID) of CP and AA in mixed diets containing multiple protein sources. Using the determined AID or SID for CP and AA in corn, soybean meal (SBM), corn distillers' dried grains with solubles (DDGS), or canola meal (CM), the AID or SID for 4 mixed diets based on corn-SBM, corn-SBM-DDGS, corn-SBM-CM, or corn-SBM-DDGS-CM were predicted and compared with determined AID or SID, respectively. Eighteen growing pigs (initial BW = 61.3 ± 5.5 kg) were surgically fitted with T-cannulas and assigned to a duplicated 9 × 4 incomplete Latin square design with 9 diets and 4 periods. The 9 experimental diets consisted of a nitrogen-free diet (NFD) to estimate basal ileal endogenous loss (BEL) of AA, 4 semipurified diets to determine the AID and SID of CP and AA in the 4 ingredients, and 4 mixed diets to test the additivity of AID and SID. Chromic oxide was added as an indigestible marker. Pigs were fed 1 of the 9 diets during each 7-d period, and ileal digesta were collected on d 6 and 7, from 0800 to 1800 h. The analyzed AA levels for the mixed diets were close to the calculated values based on the AA composition of each ingredient. The results revealed that the predicted SID were consistent with determined values, except for Leu, Thr, Asp, Cys, Pro, and Ser in the corn-SBM diet and Met and Cys in the corn-SBM-DDGS diet. The determined AID for total AA and Arg, His, Trp, Gly, and Pro in the corn-SBM diet were greater (P < 0.05) than predicted. For the corn-SBM-DDGS diet, the determined AID were greater (P < 0.05) than predicted AID for CP, total AA, and all AA except for Arg, Leu, and Pro. In the corn-SBM-CM diet, the determined AID were greater (P < 0.05) than predicted AID for Arg, Cys, and Gly. When compared with determined values, predicted AID in the corn-SBM-DDGS-CM diet were lower (P < 0.05) for total AA and Arg, Met, Cys, and Pro. In conclusion, the results substantiate the notion that SID of AA are more accurate than AID for predicting ileal digestibility of AA in mixed diets containing multiple protein sources. In addition, the lack of additivity of AID in mixed diets could be attributed to the intrinsic characteristics of the feed ingredient, especially its AA content.